Myeloid-derived suppressor cell (MDSC) key genes analysis in rat anti-CD28-induced immune tolerance kidney transplantation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33532310", "kind": "science-record", "revision": 8, "content_hash": "sha256:a8f7b838816e6255fda5e96593fd3d7fa7cd4701cc6dbc2ff9a34d202e502cd2", "created_at": "2026-11-01T15:41:24Z", "updated_at": "2026-11-01T22:03:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Myeloid-derived suppressor cell (MDSC) key genes analysis in rat anti-CD28-induced immune tolerance kidney transplantation.", "doi": "10.21037/tau-20-943", "pmid": "33532310", "authors": ["Tianying Yang", "Jiawei Li", "Yichen Jia", "Chunchen Yang", "Ruirui Sang", "Tongyu Zhu", "Ming Xu", "Ruiming Rong", "Cheng Yang"], "journal": "Translational andrology and urology", "year": 2021, "abstract": "BACKGROUND: In the field of transplantation, inducing immune tolerance in recipients is of great importance. Blocking co-stimulatory molecule using anti-CD28 antibody could induce tolerance in a rat kidney transplantation model. Myeloid-derived suppressor cells (MDSCs) reveals strong immune suppressive abilities in kidney transplantation. Here we analyzed key genes of MDSCs leading to transplant tolerance in this model.\nMETHODS: Microarray data of rat gene expression profiles under accession number GSE28545 in the Gene Expression Omnibus (GEO) database were analyzed. Running the LIMMA package in R language, the differentially expressed genes (DEGs) were found. Enrichment analysis of the DEGs was conducted in the Database for Annotation, Visualization and Integrated Discovery (DAVID) database to explore gene ontology (GO) annotation and their Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Their protein-protein interactions (PPIs) were provided by STRING database and was visualized in Cytoscape. Hub genes were carried out by CytoHubba.\nRESULTS: Three hundred and thirty-eight DEGs were exported, including 27 upregulated and 311 downregulated genes. The functions and KEGG pathways of the DEGs were assessed and the PPI network was constructed based on the string interactions of the DEGs. The network was visualized in Cytoscape; the entire PPI network consisted of 192 nodes and 469 edges. Zap70, Cdc42, Stat1, Stat4, Ccl5 and Cxcr3 were among the hub genes.\nCONCLUSIONS: These key genes, corresponding proteins and their functions may provide valuable background for both basic and clinical research and could be the direction of future studies in immune tolerance, especially those examining immunocyte-induced tolerance.", "claims": [{"id": "claim-method", "statement": "A t-test was used to compare tolerant and syngeneic samples. Two-tailed statistical tests with P≤0.05 were considered as statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532310", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "A t-test was used to compare tolerant and syngeneic samples. Two-tailed statistical tests with P≤0.05 were considered as statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "From the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), we extracted microarray data from accession number GSE28545 (species: Rattus norvegicus; platform: GPL2996; samples: GSM706861–GSM706865) (15), which compared the levels of blood MDSCs from three tolerant allogeneic kidney transplant recipients with two syngenic kidney transplant recipients at 100 days post-transplantation", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33532310", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "From the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), we extracted microarray data from accession number GSE28545 (species: Rattus norvegicus; platform: GPL2996; samples: GSM706861–GSM706865) (15), which compared the levels of blood MDSCs from three tolerant allogeneic kidney transplant recipients with two syngenic kidney transplant recipients at 100 days post-transplantation"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33532310"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE28545"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE28545"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33532310", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tau-20-943", "sha256": 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accession number GSE28545 (species: Rattus norvegicus; platform: GPL2996; samples: GSM706861–GSM706865) (15), which compared the levels of blood MDSCs from three tolerant allogeneic kidney transplant recipients with two syngenic kidney transplant recipients at 100 days post-transplantation", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "From the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), we extracted microarray data from accession number GSE28545 (species: Rattus norvegicus; platform: GPL2996; samples: GSM706861–GSM706865) (15), which compared the levels of blood MDSCs from three tolerant allogeneic kidney transplant recipients with two syngenic kidney transplant recipients at 100 days post-transplantation", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM706861", "GSM706862", "GSM706863", "GSM706864", "GSM706865"], "sample_count": 5, "group_sizes": null, 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Two-tailed statistical tests with P≤0.05 were considered as statistically significant."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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